Molecular Categorization of Some Water Yam (Dioscorea alata L.) Germplasm in Ghana Using Microsatellite (SSR) Markers

Abstract

The yam species, Dioscorea alata has an advantage for sustainable cultivation due to its comparatively good agronomic characteristics. Breeders are therefore keen to improve the food quality of the species. Nevertheless, published data on molecular classification and genetic diversity of this crop are scanty. This research therefore investigated genetic variability and relationships among some collected Ghanaian D. alata accessions (35) together with 14 introductions from IITA in Nigeria. The true genetic identity and population structure of the accessions were determined using 14 Simple Sequence Repeats primer pairs available for yams. Dimensional scatter diagram of the principal coordinates showed a wide dispersion among the accessions. Cluster analysis using unweighted neighbour-joining method clearly separated the 49 accessions into five main groupings. From the allele frequency analysis, the size of amplified alleles ranged from 100 to 510 bp. The mean polymorphic information content (PIC) values for all markers used was 0.91 and ranged between 0.86 and 0.94 in loci YM13 and YM30 respectively. Gene diversity was high and the average observed heterozygosity was 0.77. Gene diversity was high ranging from 0.87 in YM13 to 0.94 in YM30 with a mean of 0.92. Generally, the allele frequency of all the primers was below 0.95 indicating that they were all polymorphic in character. The findings of this study confirm that SSR molecular markers are able to identify closely related materials within species.

Assessing the genetic diversity of Dioscorea alata and related species from Colombia through inter-simple sequence repeat (ISSR) markers

“…Finally, high levels of genetic diversity using ISSR markers were also reported by Nascimento et al (2013) and Kung et al (2016). Other studies using SSR (Otoo et al, 2015;Arnau et al, 2017;Mulualem et al, 2018) and AFLP markers (Rivera-Jiménez et al, 2011) also reported high genetic diversity in yam.…”

Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers

“…alata using microsatellite markers. Several other studies on genetic diversity have been conducted on this species using different types of molecular markers including random amplified polymorphism DNAs [30, 55], amplified fragment length polymorphisms [15, 56, 57] and simple sequence repeat (SSR) markers [34, 58]. However, these included accessions from only one or two regions or collections.…”

“…alata collections, including RAPDs [30], AFLPs [31] and SSRs [32, 33, 34]. SSR markers (microsatellites) are considered to be the markers of choice for analyzing genetic diversity because of their co-dominance, high reproducibility, high global mutation rates and polymorphism [35, 36].…”

Development of a cost‐effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections

“…Molecular markers have been used to characterize D. alata diversity: random amplified polymorphic DNA (RAPD; Asemota, Ramser, Lopez-Peralta, Weising, & Kahl, 1996), isoenzymes (Lebot et al, 1998), amplified fragment length polymorphism (AFLP; Malapa, Arnau, Noyer, & Lebot, 2005), simple sequence repeats (SSRs; Siqueira, Marconi, Bonatelli, Zucchi, & Veasey, 2011;Sartie, Asiedu, & Franco, 2012;Otoo, Anokye, Asare, & Telleh, 2015;Chaïr et al, 2016;Arnau et al, 2017), plastid sequences , and Diversity Arrays Technology (DArT; Vandenbroucke et al, 2016).…”